User: Vitis

gravatar for Vitis
Vitis2.1k
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Location:
New York
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10 minutes ago
Joined:
7 years, 11 months ago
Email:
b*********@gmail.com

A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 304 results • page 1 of 31 • next >
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Answer: A: trouble with bedtools intersect and coverage
... As of bedtools version 2.27.1, the information for "bedtools coverage" is the following: Tool: bedtools coverage (aka coverageBed) Version: v2.27.1 Summary: Returns the depth and breadth of coverage of features from B on the intervals in A. Usage: bedtools coverage [ ...
written 5 minutes ago by Vitis2.1k
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Comment: C: JBrowse help with opening a Gff gene model file
... Thanks for clarifying that for me! ...
written 2 days ago by Vitis2.1k
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Comment: C: JBrowse help with opening a Gff gene model file
... Can you try converting the GFF3 into a json track and see what would happen? That may give you more information if anything goes wrong. Also, it is usually useful to run a GFF3 check using gff_validator, even though your GFF3 seems to be fine. http://genometools.org/cgi-bin/gff3validator.cgi ...
written 2 days ago by Vitis2.1k
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Comment: C: Insert size distribution for BWA
... Usually you could estimate the library fragment size distribution from a gel or bioanalyzer results before sequencing, then compare to the fragment size estimated by BWA. Or you may map using another read aligner and compare that estimation with BWA. ...
written 2 days ago by Vitis2.1k
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Aligner for large indels (up to 200bp out of 500bp reads)
... I'm looking for a aligner or read mapper that could handle larger indels well, up to 200bp out of 300~500bp reads. These reads are merged paired-end reads from Illumina MiSeq platform. BWA MEM seems to be working well all the way to ~60bp indels, but would just do clipping for events larger than tha ...
alignment written 3 days ago by Vitis2.1k
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Comment: C: Extract reads matching variants from VCF file
... CIGAR string does not only contain the operations (D, I, etc) but also the length of the operation. By comparing the length with the indel size in VCF, maybe you would be able to count the reads that support the specific indel in question. I usually use pysam for this kind of CIGAR queries. https: ...
written 5 days ago by Vitis2.1k
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Answer: A: SNP calling with de novo assembly
... Would you describe your objectives a bit more clearly? Are you trying to conduct comparative genomics across the strains, or simply calling variants among these strains? If your strains are closely related, you may choose one strain as a reference, and use minimap2 to align contigs of other strains ...
written 5 days ago by Vitis2.1k
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Comment: C: Visualizing Orthologs and Paralogs genes
... A very interesting question! By definition, orthologs and paralogs are defined by comparing evolutionary relationships among genes to evolutionary relationships among species. Genes strictly follow species trees are orthologs. I would think a good visualization of orhologs and paralogs may involve p ...
written 23 days ago by Vitis2.1k
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Answer: A: Improve illumina short read assembly using PacBio long reads
... filtlong may help you filter and correct long reads using your short reads. https://github.com/rrwick/Filtlong Then the corrected long reads may help you scaffold some contigs. But I agree with the other answers: 1.5X of long reads wouldn't get you very far. ...
written 24 days ago by Vitis2.1k
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Comment: C: GATK genomicsDBimport intervals for WGS
... Running these steps for each chromosome is largely because there is no enough computational resources for running the entire genome in one shot. If you do run them separately, I think you need to run it in separate commands and use different workspace path. ...
written 24 days ago by Vitis2.1k

Latest awards to Vitis

Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 4 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 5 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 7 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 8 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 2.4 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.
Guru 5.2 years ago, received more than 100 upvotes.
Centurion 5.2 years ago, created 100 posts.
Supporter 5.2 years ago, voted at least 25 times.
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Appreciated 7.2 years ago, created a post with more than 5 votes. For A: Rna-Seq Data Variant Calling
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Data Variant Calling
Student 7.2 years ago, asked a question with at least 3 up-votes. For Genomic Read Mapping Biased Towards Coding Regions?

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